1.
Glutamine
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Glutamine is an α-amino acid that is used in the biosynthesis of proteins. In human blood, glutamine is the most abundant free amino acid, Glutamine plays a role in a variety of biochemical functions, Protein synthesis, as any other of the 20 proteinogenic amino acids Lipid synthesis, especially by cancer cells. Glutamine is synthesized by the enzyme glutamine synthetase from glutamate and ammonia, the most relevant glutamine-producing tissue is the muscle mass, accounting for about 90% of all glutamine synthesized. Glutamine is also released, in amounts, by the lungs. The most eager consumers of glutamine are the cells of intestines, the cells for the acid-base balance, activated immune cells. In states where tissue is being built or repaired, like growth of infants, or healing from wounds or severe illness. Glutamine is the most abundant naturally occurring, nonessential amino acid in the human body, in the body, it is found circulating in the blood, as well as stored in the skeletal muscles. It becomes conditionally essential in states of illness or injury, humans obtain glutamine through catabolism of proteins in foods they eat. Glutamine mouthwash may be useful to prevent oral mucositis in people undergoing chemotherapy, supplementation does not appear to be useful in adults or children with Crohns disease or inflammatory bowel disease but clinical studies as of 2016 were underpowered. Supplementation does not appear to have an effect in infants with significant problems of the stomach or intestines, isoglutamine Glutamine spectra acquired through mass spectroscopy
2.
Glutaric acid
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Glutaric acid is the organic compound with the formula C3H62. Although the related linear dicarboxylic acids adipic and succinic acids are only to a few percent at room temperature. Glutaric acid is produced in the body during the metabolism of some amino acids, including lysine. Defects in this pathway can lead to a disorder called glutaric aciduria. Glutaric acid can be prepared by the ring-opening of butyrolactone with potassium cyanide to give the mixed potassium carboxylate-nitrile that is hydrolyzed to the diacid, alternatively hydrolysis, followed by oxidation of dihydropyran gives glutaric acid. It can also be prepared from reacting 1, 3-dibromopropane with sodium or potassium cyanide to obtain the dinitrile,1, 5-Pentanediol, a common plasticizer and precursor to polyesters is manufactured by hydrogenation of glutaric acid and its derivatives. Glutaric acid itself has used in the production of polymers such as polyester polyols. The odd number of atoms is useful in decreasing polymer elasticity. Uvitonic acid is obtained by the action of ammonia on pyrotartaric acid, glutaric acid may cause irritation to the skin and eyes. Acute hazards include the fact that this compound may be harmful by ingestion, inhalation or skin absorption, calculator, Water and solute activities in aqueous glutaric acid
3.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
4.
ChEMBL
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ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute, of the European Molecular Biology Laboratory, based at the Wellcome Trust Genome Campus, Hinxton, the database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, the ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50, data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 was launched in January 2010, including 2.4 million bioassay measurements covering 622,824 compounds and this was obtained from curating over 34,000 publications across twelve medicinal chemistry journals. ChEMBLs coverage of available bioactivity data has grown to become the most comprehensive ever seen in a public database, in October 2010 ChEMBL version 8 was launched, with over 2.97 million bioassay measurements covering 636,269 compounds. ChEMBL_10 saw the addition of the PubChem confirmatory assays, in order to integrate data that is comparable to the type, ChEMBLdb can be accessed via a web interface or downloaded by File Transfer Protocol. It is formatted in a manner amenable to computerized data mining, ChEMBL is also integrated into other large-scale chemistry resources, including PubChem and the ChemSpider system of the Royal Society of Chemistry. In addition to the database, the ChEMBL group have developed tools and these include Kinase SARfari, an integrated chemogenomics workbench focussed on kinases. The system incorporates and links sequence, structure, compounds and screening data, the primary purpose of ChEMBL-NTD is to provide a freely accessible and permanent archive and distribution centre for deposited data. July 2012 saw the release of a new data service, sponsored by the Medicines for Malaria Venture. The data in this service includes compounds from the Malaria Box screening set, myChEMBL, the ChEMBL virtual machine, was released in October 2013 to allow users to access a complete and free, easy-to-install cheminformatics infrastructure. In December 2013, the operations of the SureChem patent informatics database were transferred to EMBL-EBI, in a portmanteau, SureChem was renamed SureChEMBL. 2014 saw the introduction of the new resource ADME SARfari - a tool for predicting and comparing cross-species ADME targets
5.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses
6.
European Chemicals Agency
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ECHA is the driving force among regulatory authorities in implementing the EUs chemicals legislation. ECHA helps companies to comply with the legislation, advances the safe use of chemicals, provides information on chemicals and it is located in Helsinki, Finland. The Agency, headed by Executive Director Geert Dancet, started working on 1 June 2007, the REACH Regulation requires companies to provide information on the hazards, risks and safe use of chemical substances that they manufacture or import. Companies register this information with ECHA and it is freely available on their website. So far, thousands of the most hazardous and the most commonly used substances have been registered, the information is technical but gives detail on the impact of each chemical on people and the environment. This also gives European consumers the right to ask whether the goods they buy contain dangerous substances. The Classification, Labelling and Packaging Regulation introduces a globally harmonised system for classifying and labelling chemicals into the EU. This worldwide system makes it easier for workers and consumers to know the effects of chemicals, companies need to notify ECHA of the classification and labelling of their chemicals. So far, ECHA has received over 5 million notifications for more than 100000 substances, the information is freely available on their website. Consumers can check chemicals in the products they use, Biocidal products include, for example, insect repellents and disinfectants used in hospitals. The Biocidal Products Regulation ensures that there is information about these products so that consumers can use them safely. ECHA is responsible for implementing the regulation, the law on Prior Informed Consent sets guidelines for the export and import of hazardous chemicals. Through this mechanism, countries due to hazardous chemicals are informed in advance and have the possibility of rejecting their import. Substances that may have effects on human health and the environment are identified as Substances of Very High Concern 1. These are mainly substances which cause cancer, mutation or are toxic to reproduction as well as substances which persist in the body or the environment, other substances considered as SVHCs include, for example, endocrine disrupting chemicals. Companies manufacturing or importing articles containing these substances in a concentration above 0 and they are required to inform users about the presence of the substance and therefore how to use it safely. Consumers have the right to ask the retailer whether these substances are present in the products they buy, once a substance has been officially identified in the EU as being of very high concern, it will be added to a list. This list is available on ECHA’s website and shows consumers and industry which chemicals are identified as SVHCs, Substances placed on the Candidate List can then move to another list
7.
E number
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E numbers are codes for substances that are permitted to be used as food additives for use within the European Union and Switzerland. Commonly found on labels, their safety assessment and approval are the responsibility of the European Food Safety Authority. Having a single unified list for food additives was first agreed upon in 1962 with food colouring, in 1964, the directives for preservatives were added,1970 for antioxidants and 1974 for the emulsifiers, stabilisers, thickeners and gelling agents. They are increasingly, though rarely, found on North American packaging. In some European countries, E number is used informally as a pejorative term for artificial food additives. This is incorrect, because many components of foods have E numbers, e. g. vitamin C. NB, Not all examples of a fall into the given numeric range. Moreover, many chemicals, particularly in the E400–499 range, have a variety of purposes, the list shows all components that have or had an E-number assigned. Not all additives listed are still allowed in the EU, but are listed as they used to have an E-number, for an overview of currently allowed additives see here. Includes Lists of authorised food additives Food additives database
8.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure
9.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES
10.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
11.
Density
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The density, or more precisely, the volumetric mass density, of a substance is its mass per unit volume. The symbol most often used for density is ρ, although the Latin letter D can also be used. Mathematically, density is defined as mass divided by volume, ρ = m V, where ρ is the density, m is the mass, and V is the volume. In some cases, density is defined as its weight per unit volume. For a pure substance the density has the numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity, osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. Thus a relative density less than one means that the floats in water. The density of a material varies with temperature and pressure and this variation is typically small for solids and liquids but much greater for gases. Increasing the pressure on an object decreases the volume of the object, increasing the temperature of a substance decreases its density by increasing its volume. In most materials, heating the bottom of a results in convection of the heat from the bottom to the top. This causes it to rise relative to more dense unheated material, the reciprocal of the density of a substance is occasionally called its specific volume, a term sometimes used in thermodynamics. Density is a property in that increasing the amount of a substance does not increase its density. Archimedes knew that the irregularly shaped wreath could be crushed into a cube whose volume could be calculated easily and compared with the mass, upon this discovery, he leapt from his bath and ran naked through the streets shouting, Eureka. As a result, the term eureka entered common parlance and is used today to indicate a moment of enlightenment, the story first appeared in written form in Vitruvius books of architecture, two centuries after it supposedly took place. Some scholars have doubted the accuracy of this tale, saying among other things that the method would have required precise measurements that would have been difficult to make at the time, from the equation for density, mass density has units of mass divided by volume. As there are units of mass and volume covering many different magnitudes there are a large number of units for mass density in use. The SI unit of kilogram per metre and the cgs unit of gram per cubic centimetre are probably the most commonly used units for density.1,000 kg/m3 equals 1 g/cm3. In industry, other larger or smaller units of mass and or volume are often more practical, see below for a list of some of the most common units of density
12.
Melting point
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The melting point of a solid is the temperature at which it changes state from solid to liquid at atmospheric pressure. At the melting point the solid and liquid phase exist in equilibrium, the melting point of a substance depends on pressure and is usually specified at standard pressure. When considered as the temperature of the change from liquid to solid. Because of the ability of some substances to supercool, the point is not considered as a characteristic property of a substance. For most substances, melting and freezing points are approximately equal, for example, the melting point and freezing point of mercury is 234.32 kelvins. However, certain substances possess differing solid-liquid transition temperatures, for example, agar melts at 85 °C and solidifies from 31 °C to 40 °C, such direction dependence is known as hysteresis. The melting point of ice at 1 atmosphere of pressure is close to 0 °C. In the presence of nucleating substances the freezing point of water is the same as the melting point, the chemical element with the highest melting point is tungsten, at 3687 K, this property makes tungsten excellent for use as filaments in light bulbs. Many laboratory techniques exist for the determination of melting points, a Kofler bench is a metal strip with a temperature gradient. Any substance can be placed on a section of the strip revealing its thermal behaviour at the temperature at that point, differential scanning calorimetry gives information on melting point together with its enthalpy of fusion. A basic melting point apparatus for the analysis of crystalline solids consists of an oil bath with a transparent window, the several grains of a solid are placed in a thin glass tube and partially immersed in the oil bath. The oil bath is heated and with the aid of the melting of the individual crystals at a certain temperature can be observed. In large/small devices, the sample is placed in a heating block, the measurement can also be made continuously with an operating process. For instance, oil refineries measure the point of diesel fuel online, meaning that the sample is taken from the process. This allows for more frequent measurements as the sample does not have to be manually collected, for refractory materials the extremely high melting point may be determined by heating the material in a black body furnace and measuring the black-body temperature with an optical pyrometer. For the highest melting materials, this may require extrapolation by several hundred degrees, the spectral radiance from an incandescent body is known to be a function of its temperature. An optical pyrometer matches the radiance of a body under study to the radiance of a source that has been previously calibrated as a function of temperature, in this way, the measurement of the absolute magnitude of the intensity of radiation is unnecessary. However, known temperatures must be used to determine the calibration of the pyrometer, for temperatures above the calibration range of the source, an extrapolation technique must be employed
13.
Aqueous solution
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An aqueous solution is a solution in which the solvent is water. It is usually shown in chemical equations by appending to the relevant chemical formula, for example, a solution of table salt, or sodium chloride, in water would be represented as Na+ + Cl−. The word aqueous means pertaining to, related to, similar to, as water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry. Substances that are hydrophobic often do not dissolve well in water, an example of a hydrophilic substance is sodium chloride. Acids and bases are aqueous solutions, as part of their Arrhenius definitions, the ability of a substance to dissolve in water is determined by whether the substance can match or exceed the strong attractive forces that water molecules generate between themselves. If the substance lacks the ability to dissolve in water the molecules form a precipitate, reactions in aqueous solutions are usually metathesis reactions. Metathesis reactions are another term for double-displacement, that is, when a cation displaces to form a bond with the other anion. The cation bonded with the latter anion will dissociate and bond with the other anion, aqueous solutions that conduct electric current efficiently contain strong electrolytes, while ones that conduct poorly are considered to have weak electrolytes. Those strong electrolytes are substances that are ionized in water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity, examples include sugar, urea, glycerol, and methylsulfonylmethane. When writing the equations of reactions, it is essential to determine the precipitate. To determine the precipitate, one must consult a chart of solubility, soluble compounds are aqueous, while insoluble compounds are the precipitate. Remember that there may not always be a precipitate, when performing calculations regarding the reacting of one or more aqueous solutions, in general one must know the concentration, or molarity, of the aqueous solutions. Solution concentration is given in terms of the form of the prior to it dissolving. Metal ions in aqueous solution Solubility Dissociation Acid-base reaction theories Properties of water Zumdahl S.1997, 4th ed. Boston, Houghton Mifflin Company
14.
Solubility
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Solubility is the property of a solid, liquid, or gaseous chemical substance called solute to dissolve in a solid, liquid, or gaseous solvent. The solubility of a substance depends on the physical and chemical properties of the solute and solvent as well as on temperature, pressure. The solubility of a substance is a different property from the rate of solution. Most often, the solvent is a liquid, which can be a substance or a mixture. One may also speak of solid solution, but rarely of solution in a gas, the extent of solubility ranges widely, from infinitely soluble such as ethanol in water, to poorly soluble, such as silver chloride in water. The term insoluble is often applied to poorly or very poorly soluble compounds, a common threshold to describe something as insoluble is less than 0.1 g per 100 mL of solvent. Under certain conditions, the solubility can be exceeded to give a so-called supersaturated solution. Metastability of crystals can also lead to apparent differences in the amount of a chemical that dissolves depending on its form or particle size. A supersaturated solution generally crystallises when seed crystals are introduced and rapid equilibration occurs, phenylsalicylate is one such simple observable substance when fully melted and then cooled below its fusion point. Solubility is not to be confused with the ability to dissolve a substance, for example, zinc dissolves in hydrochloric acid as a result of a chemical reaction releasing hydrogen gas in a displacement reaction. The zinc ions are soluble in the acid, the smaller a particle is, the faster it dissolves although there are many factors to add to this generalization. Crucially solubility applies to all areas of chemistry, geochemistry, inorganic, physical, organic, in all cases it will depend on the physical conditions and the enthalpy and entropy directly relating to the solvents and solutes concerned. By far the most common solvent in chemistry is water which is a solvent for most ionic compounds as well as a range of organic substances. This is a factor in acidity/alkalinity and much environmental and geochemical work. According to the IUPAC definition, solubility is the composition of a saturated solution expressed as a proportion of a designated solute in a designated solvent. Solubility may be stated in units of concentration such as molarity, molality, mole fraction, mole ratio, mass per volume. Solubility occurs under dynamic equilibrium, which means that solubility results from the simultaneous and opposing processes of dissolution, the solubility equilibrium occurs when the two processes proceed at a constant rate. The term solubility is used in some fields where the solute is altered by solvolysis
15.
Acid dissociation constant
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An acid dissociation constant, Ka, is a quantitative measure of the strength of an acid in solution. It is the constant for a chemical reaction known as dissociation in the context of acid–base reactions. In the example shown in the figure, HA represents acetic acid, and A− represents the acetate ion, the chemical species HA, A− and H3O+ are said to be in equilibrium when their concentrations do not change with the passing of time. The definition can then be more simply H A ⇌ A − + H +, K a = This is the definition in common usage. A weak acid has a pKa value in the approximate range −2 to 12 in water, pKa values for strong acids can, however, be estimated by theoretical means. The definition can be extended to non-aqueous solvents, such as acetonitrile and dimethylsulfoxide. Denoting a solvent molecule by S H A + S ⇌ A − + S H +, K a = When the concentration of solvent molecules can be taken to be constant, K a =, as before. The value of pKa also depends on structure of the acid in many ways. For example, Pauling proposed two rules, one for successive pKa of polyprotic acids, and one to estimate the pKa of oxyacids based on the number of =O and −OH groups. Other structural factors that influence the magnitude of the dissociation constant include inductive effects, mesomeric effects. Hammett type equations have frequently applied to the estimation of pKa. The quantitative behaviour of acids and bases in solution can be only if their pKa values are known. These calculations find application in different areas of chemistry, biology, medicine. Acid dissociation constants are essential in aquatic chemistry and chemical oceanography. In living organisms, acid–base homeostasis and enzyme kinetics are dependent on the pKa values of the acids and bases present in the cell. According to Arrheniuss original definition, an acid is a substance that dissociates in solution, releasing the hydrogen ion H+. The equilibrium constant for this reaction is known as a dissociation constant. Brønsted and Lowry generalised this further to an exchange reaction
16.
Safety data sheet
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A safety data sheet, material safety data sheet, or product safety data sheet is an important component of product stewardship, occupational safety and health, and spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements, SDSs are a widely used system for cataloging information on chemicals, chemical compounds, and chemical mixtures. SDS information may include instructions for the use and potential hazards associated with a particular material or product. The SDS should be available for reference in the area where the chemicals are being stored or in use, there is also a duty to properly label substances on the basis of physico-chemical, health and/or environmental risk. Labels can include hazard symbols such as the European Union standard symbols, a SDS for a substance is not primarily intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. It is important to use an SDS specific to country and supplier, as the same product can have different formulations in different countries. The formulation and hazard of a product using a name may vary between manufacturers in the same country. Safety data sheets have made an integral part of the system of Regulation No 1907/2006. The SDS must be supplied in a language of the Member State where the substance or mixture is placed on the market. The 16 sections are, SECTION1, Identification of the substance/mixture, relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4, Emergency telephone number SECTION2, Hazards identification 2.1. Classification of the substance or mixture 2.2, Other hazards SECTION3, Composition/information on ingredients 3.1. Mixtures SECTION4, First aid measures 4.1, Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3, indication of any immediate medical attention and special treatment needed SECTION5, Firefighting measures 5.1. Special hazards arising from the substance or mixture 5.3, advice for firefighters SECTION6, Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2, methods and material for containment and cleaning up 6.4. Reference to other sections SECTION7, Handling and storage 7.1, conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION8, Exposure controls/personal protection 8.1, Exposure controls SECTION9, Physical and chemical properties 9.1
17.
Refractive index
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In optics, the refractive index or index of refraction n of a material is a dimensionless number that describes how light propagates through that medium. It is defined as n = c v, where c is the speed of light in vacuum, for example, the refractive index of water is 1.333, meaning that light travels 1.333 times faster in a vacuum than it does in water. The refractive index determines how light is bent, or refracted. The refractive indices also determine the amount of light that is reflected when reaching the interface, as well as the angle for total internal reflection. This implies that vacuum has a index of 1. The refractive index varies with the wavelength of light and this is called dispersion and causes the splitting of white light into its constituent colors in prisms and rainbows, and chromatic aberration in lenses. Light propagation in absorbing materials can be described using a refractive index. The imaginary part then handles the attenuation, while the real part accounts for refraction, the concept of refractive index is widely used within the full electromagnetic spectrum, from X-rays to radio waves. It can also be used with wave phenomena such as sound, in this case the speed of sound is used instead of that of light and a reference medium other than vacuum must be chosen. Thomas Young was presumably the person who first used, and invented, at the same time he changed this value of refractive power into a single number, instead of the traditional ratio of two numbers. The ratio had the disadvantage of different appearances, newton, who called it the proportion of the sines of incidence and refraction, wrote it as a ratio of two numbers, like 529 to 396. Hauksbee, who called it the ratio of refraction, wrote it as a ratio with a fixed numerator, hutton wrote it as a ratio with a fixed denominator, like 1.3358 to 1. Young did not use a symbol for the index of refraction, in the next years, others started using different symbols, n, m, and µ. For visible light most transparent media have refractive indices between 1 and 2, a few examples are given in the adjacent table. These values are measured at the yellow doublet D-line of sodium, with a wavelength of 589 nanometers, gases at atmospheric pressure have refractive indices close to 1 because of their low density. Almost all solids and liquids have refractive indices above 1.3, aerogel is a very low density solid that can be produced with refractive index in the range from 1.002 to 1.265. Moissanite lies at the end of the range with a refractive index as high as 2.65. Most plastics have refractive indices in the range from 1.3 to 1.7, for infrared light refractive indices can be considerably higher
18.
Relative permittivity
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The relative permittivity of a material is its permittivity expressed as a ratio relative to the permittivity of vacuum. Permittivity is a property that affects the Coulomb force between two point charges in the material. Relative permittivity is the factor by which the field between the charges is decreased relative to vacuum. Likewise, relative permittivity is the ratio of the capacitance of a capacitor using that material as a dielectric, relative permittivity is also commonly known as dielectric constant, a term deprecated in physics and engineering as well as in chemistry. Relative permittivity is typically denoted as εr and is defined as ε r = ε ε0, where ε is the complex frequency-dependent absolute permittivity of the material, and ε0 is the vacuum permittivity. Relative permittivity is a number that is in general complex-valued, its real and imaginary parts are denoted as. The relative permittivity of a medium is related to its electric susceptibility, χe, in anisotropic media the relative permittivity is a second rank tensor. The relative permittivity of a material for a frequency of zero is known as its relative permittivity. The historical term for the relative permittivity is dielectric constant and it is still commonly used, but has been deprecated by standards organizations, because of its ambiguity, as some older authors used it for the absolute permittivity ε. The permittivity may be quoted either as a property or as a frequency-dependent variant. It has also used to refer to only the real component εr of the complex-valued relative permittivity. In the causal theory of waves, permittivity is a complex quantity, the imaginary part corresponds to a phase shift of the polarization P relative to E and leads to the attenuation of electromagnetic waves passing through the medium. By definition, the relative permittivity of vacuum is equal to 1. The relative static permittivity, εr, can be measured for static electric fields as follows, first the capacitance of a test capacitor, then, using the same capacitor and distance between its plates, the capacitance Cx with a dielectric between the plates is measured. The relative dielectric constant can be calculated as ε r = C x C0. For time-variant electromagnetic fields, this quantity becomes frequency-dependent, an indirect technique to calculate εr is conversion of radio frequency S-parameter measurement results. A description of frequently used S-parameter conversions for determination of the frequency-dependent εr of dielectrics can be found in this bibliographic source, alternatively, resonance based effects may be employed at fixed frequencies. The relative permittivity is a piece of information when designing capacitors
19.
Infrared spectroscopy
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Infrared spectroscopy involves the interaction of infrared radiation with matter. It covers a range of techniques, mostly based on absorption spectroscopy, as with all spectroscopic techniques, it can be used to identify and study chemicals. Sample may be solid, liquid, or gas, the method or technique of infrared spectroscopy is conducted with an instrument called an infrared spectrometer to produce an infrared spectrum. An IR spectrum is essentially a graph of infrared light absorbance on the vertical axis vs. frequency or wavelength on the horizontal axis, typical units of frequency used in IR spectra are reciprocal centimeters, with the symbol cm−1. Units of IR wavelength are commonly given in micrometers, symbol μm, a common laboratory instrument that uses this technique is a Fourier transform infrared spectrometer. Two-dimensional IR is also possible as discussed below, the infrared portion of the electromagnetic spectrum is usually divided into three regions, the near-, mid- and far- infrared, named for their relation to the visible spectrum. The higher-energy near-IR, approximately 14000–4000 cm−1 can excite overtone or harmonic vibrations, the mid-infrared, approximately 4000–400 cm−1 may be used to study the fundamental vibrations and associated rotational-vibrational structure. The far-infrared, approximately 400–10 cm−1, lying adjacent to the region, has low energy. The names and classifications of these subregions are conventions, and are loosely based on the relative molecular or electromagnetic properties. Infrared spectroscopy exploits the fact that molecules absorb frequencies that are characteristic of their structure and these absorptions occur at resonant frequencies, i. e. the frequency of the absorbed radiation matches the vibrational frequency. The energies are affected by the shape of the potential energy surfaces, the masses of the atoms. In particular, in the Born–Oppenheimer and harmonic approximations, i. e, the resonant frequencies are also related to the strength of the bond and the mass of the atoms at either end of it. Thus, the frequency of the vibrations are associated with a normal mode of motion. In order for a mode in a sample to be IR active. A permanent dipole is not necessary, as the rule requires only a change in dipole moment, a molecule can vibrate in many ways, and each way is called a vibrational mode. For molecules with N number of atoms, linear molecules have 3N –5 degrees of vibrational modes, as an example H2O, a non-linear molecule, will have 3 ×3 –6 =3 degrees of vibrational freedom, or modes. Simple diatomic molecules have only one bond and only one vibrational band, if the molecule is symmetrical, e. g. N2, the band is not observed in the IR spectrum, but only in the Raman spectrum. Asymmetrical diatomic molecules, e. g. CO, absorb in the IR spectrum, more complex molecules have many bonds, and their vibrational spectra are correspondingly more complex, i. e. big molecules have many peaks in their IR spectra
20.
Nuclear magnetic resonance spectroscopy
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Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei. This type of spectroscopy determines the physical and chemical properties of atoms or the molecules in which they are contained and it relies on the phenomenon of nuclear magnetic resonance and can provide detailed information about the structure, dynamics, reaction state, and chemical environment of molecules. Suitable samples range from small compounds analyzed with 1-dimensional proton or carbon-13 NMR spectroscopy to large proteins or nucleic acids using 3 or 4-dimensional techniques. The impact of NMR spectroscopy on the sciences has been substantial because of the range of information, NMR spectra are unique, well-resolved, analytically tractable and often highly predictable for small molecules. Thus, in organic chemistry practice, NMR analysis is used to confirm the identity of a substance, different functional groups are obviously distinguishable, and identical functional groups with differing neighboring substituents still give distinguishable signals. NMR has largely replaced traditional wet chemistry tests such as reagents or typical chromatography for identification. A disadvantage is that a large amount, 2–50 mg, of a purified substance is required. Preferably, the sample should be dissolved in a solvent, because NMR analysis of solids requires a dedicated MAS machine, the timescale of NMR is relatively long, and thus it is not suitable for observing fast phenomena, producing only an averaged spectrum. NMR spectrometers are relatively expensive, universities usually have them, modern NMR spectrometers have a very strong, large and expensive liquid helium-cooled superconducting magnet, because resolution directly depends on magnetic field strength. There are even benchtop NMR spectrometers, the Purcell group at Harvard University and the Bloch group at Stanford University independently developed NMR spectroscopy in the late 1940s and early 1950s. Edward Mills Purcell and Felix Bloch shared the 1952 Nobel Prize in Physics for their discoveries, when placed in a magnetic field, NMR active nuclei absorb electromagnetic radiation at a frequency characteristic of the isotope. The resonant frequency, energy of the absorption, and the intensity of the signal are proportional to the strength of the magnetic field, for example, in a 21 Tesla magnetic field, protons resonate at 900 MHz. It is common to refer to a 21 T magnet as a 900 MHz magnet, spinning the sample is necessary to average out diffusional motion. Whereas, measurements of diffusion constants are done the sample stationary and spinning off, the vast majority of nuclei in a solution would belong to the solvent, and most regular solvents are hydrocarbons and would contain NMR-reactive protons. The most used deuterated solvent is deuterochloroform, although deuterium oxide and deuterated DMSO are used for hydrophilic analytes, the chemical shifts are slightly different in different solvents, depending on electronic solvation effects. NMR spectra are often calibrated against the known solvent residual proton peak instead of added tetramethylsilane, to detect the very small frequency shifts due to nuclear magnetic resonance, the applied magnetic field must be constant throughout the sample volume. High resolution NMR spectrometers use shims to adjust the homogeneity of the field to parts per billion in a volume of a few cubic centimeters. In order to detect and compensate for inhomogeneity and drift in the magnetic field, in modern NMR spectrometers shimming is adjusted automatically, though in some cases the operator has to optimize the shim parameters manually to obtain the best possible resolution
21.
Mass spectrometry
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Mass spectrometry is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. In simpler terms, a mass spectrum measures the masses within a sample, mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio, in a typical MS procedure, a sample, which may be solid, liquid, or gas, is ionized, for example by bombarding it with electrons. This may cause some of the molecules to break into charged fragments. The ions are detected by a capable of detecting charged particles. Results are displayed as spectra of the abundance of detected ions as a function of the mass-to-charge ratio. The atoms or molecules in the sample can be identified by correlating known masses to the masses or through a characteristic fragmentation pattern. Goldstein called these positively charged anode rays Kanalstrahlen, the translation of this term into English is canal rays. Wien found that the charge-to-mass ratio depended on the nature of the gas in the discharge tube, thomson later improved on the work of Wien by reducing the pressure to create the mass spectrograph. The word spectrograph had become part of the international scientific vocabulary by 1884, a mass spectroscope is similar to a mass spectrograph except that the beam of ions is directed onto a phosphor screen. A mass spectroscope configuration was used in early instruments when it was desired that the effects of adjustments be quickly observed, once the instrument was properly adjusted, a photographic plate was inserted and exposed. The term mass spectroscope continued to be used though the direct illumination of a phosphor screen was replaced by indirect measurements with an oscilloscope. The use of the mass spectroscopy is now discouraged due to the possibility of confusion with light spectroscopy. Mass spectrometry is often abbreviated as mass-spec or simply as MS, modern techniques of mass spectrometry were devised by Arthur Jeffrey Dempster and F. W. Aston in 1918 and 1919 respectively. Sector mass spectrometers known as calutrons were used for separating the isotopes of uranium developed by Ernest O. Lawrence during the Manhattan Project, calutron mass spectrometers were used for uranium enrichment at the Oak Ridge, Tennessee Y-12 plant established during World War II. In 1989, half of the Nobel Prize in Physics was awarded to Hans Dehmelt, a mass spectrometer consists of three components, an ion source, a mass analyzer, and a detector. The ionizer converts a portion of the sample into ions, there is a wide variety of ionization techniques, depending on the phase of the sample and the efficiency of various ionization mechanisms for the unknown species. An extraction system removes ions from the sample, which are then targeted through the mass analyzer, the differences in masses of the fragments allows the mass analyzer to sort the ions by their mass-to-charge ratio
22.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
23.
Carboxylic acid
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A carboxylic acid /ˌkɑːrbɒkˈsɪlɪk/ is an organic compound that contains a carboxyl group. The general formula of an acid is R–COOH, with R referring to the rest of the molecule. Carboxylic acids occur widely and include the amino acids and acetic acid, salts and esters of carboxylic acids are called carboxylates. When a carboxyl group is deprotonated, its conjugate base forms a carboxylate anion, carboxylate ions are resonance-stabilized, and this increased stability makes carboxylic acids more acidic than alcohols. Carboxylic acids can be seen as reduced or alkylated forms of the Lewis acid carbon dioxide, carboxylic acids are commonly identified using their trivial names, and usually have the suffix -ic acid. IUPAC-recommended names also exist, in system, carboxylic acids have an -oic acid suffix. For example, butyric acid is butanoic acid by IUPAC guidelines, the -oic acid nomenclature detail is based on the name of the previously-known chemical benzoic acid. Alternately, it can be named as a carboxy or carboxylic acid substituent on another parent structure, for example, 2-carboxyfuran. The carboxylate anion of an acid is usually named with the suffix -ate, in keeping with the general pattern of -ic acid and -ate for a conjugate acid and its conjugate base. For example, the base of acetic acid is acetate. The radical •COOH has only a fleeting existence. The acid dissociation constant of •COOH has been measured using electron paramagnetic resonance spectroscopy, the carboxyl group tends to dimerise to form oxalic acid. Because they are both hydrogen-bond acceptors and hydrogen-bond donors, they participate in hydrogen bonding. Together the hydroxyl and carbonyl group forms the functional group carboxyl, carboxylic acids usually exist as dimeric pairs in nonpolar media due to their tendency to self-associate. Smaller carboxylic acids are soluble in water, whereas higher carboxylic acids are less due to the increasing hydrophobic nature of the alkyl chain. These longer chain acids tend to be soluble in less-polar solvents such as ethers. Carboxylic acids tend to have higher boiling points than water, not only because of their surface area. Carboxylic acids tend to evaporate or boil as these dimers, for boiling to occur, either the dimer bonds must be broken or the entire dimer arrangement must be vaporised, both of which increase the enthalpy of vaporization requirements significantly
24.
Amine
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In organic chemistry, amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group, important amines include amino acids, biogenic amines, trimethylamine, and aniline, see Category, Amines for a list of amines. Inorganic derivatives of ammonia are also called amines, such as chloramine, see Category, compounds with a nitrogen atom attached to a carbonyl group, thus having the structure R–CO–NR′R″, are called amides and have different chemical properties from amines. An aliphatic amine has no aromatic ring attached directly to the nitrogen atom, aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents, the presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect. Amines are organized into four subcategories, Primary amines — Primary amines arise when one of three atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, Secondary amines — Secondary amines have two organic substituents bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine, tertiary amines — In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a fishy smell. Cyclic amines — Cyclic amines are either secondary or tertiary amines, examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of tertiary amines. It is also possible to have four organic substituents on the nitrogen and these species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions, Amines are named in several ways. Typically, the compound is given the prefix amino- or the suffix, the prefix N- shows substitution on the nitrogen atom. An organic compound with multiple amino groups is called a diamine, triamine, tetraamine, systematic names for some common amines, Hydrogen bonding significantly influences the properties of primary and secondary amines. Thus the melting point and boiling point of amines is higher than those of the corresponding phosphines, for example, methyl and ethyl amines are gases under standard conditions, whereas the corresponding methyl and ethyl alcohols are liquids. Amines possess a characteristic smell, liquid amines have a distinctive fishy smell. The nitrogen atom features a lone pair that can bind H+ to form an ammonium ion R3NH+
25.
Acid
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An acid is a molecule or ion capable of donating a hydron, or, alternatively, capable of forming a covalent bond with an electron pair. The first category of acids is the donors or Brønsted acids. In the special case of solutions, proton donors form the hydronium ion H3O+ and are known as Arrhenius acids. Brønsted and Lowry generalized the Arrhenius theory to include non-aqueous solvents, acids form aqueous solutions with a sour taste, can turn blue litmus red, and react with bases and certain metals to form salts. The word acid is derived from the Latin acidus/acēre meaning sour, an aqueous solution of an acid has a pH less than 7 and is colloquially also referred to as acid, while the strict definition refers only to the solute. A lower pH means a higher acidity, and thus a higher concentration of hydrogen ions in the solution. Chemicals or substances having the property of an acid are said to be acidic, common aqueous acids include hydrochloric acid, acetic acid, sulfuric acid, and citric acid. As these examples show, acids can be solutions or pure substances, strong acids and some concentrated weak acids are corrosive, but there are exceptions such as carboranes and boric acid. The second category of acids are Lewis acids, which form a covalent bond with an electron pair, however, hydrogen chloride, acetic acid, and most other Brønsted-Lowry acids cannot form a covalent bond with an electron pair and are therefore not Lewis acids. Conversely, many Lewis acids are not Arrhenius or Brønsted-Lowry acids, in modern terminology, an acid is implicitly a Brønsted acid and not a Lewis acid, since chemists almost always refer to a Lewis acid explicitly as a Lewis acid. Modern definitions are concerned with the chemical reactions common to all acids. Most acids encountered in life are aqueous solutions, or can be dissolved in water, so the Arrhenius. The Brønsted-Lowry definition is the most widely used definition, unless otherwise specified, hydronium ions are acids according to all three definitions. Interestingly, although alcohols and amines can be Brønsted-Lowry acids, they can function as Lewis bases due to the lone pairs of electrons on their oxygen and nitrogen atoms. The Swedish chemist Svante Arrhenius attributed the properties of acidity to hydrogen ions or protons in 1884, an Arrhenius acid is a substance that, when added to water, increases the concentration of H+ ions in the water. Thus, an Arrhenius acid can also be described as a substance that increases the concentration of ions when added to water. Examples include molecular substances such as HCl and acetic acid, an Arrhenius base, on the other hand, is a substance which increases the concentration of hydroxide ions when dissolved in water. Thus, an Arrhenius acid could also be said to be one that decreases hydroxide concentration, in an acidic solution, the concentration of hydronium ions is greater than 10−7 moles per liter
26.
Electric charge
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Electric charge is the physical property of matter that causes it to experience a force when placed in an electromagnetic field. There are two types of charges, positive and negative. Like charges repel and unlike attract, an absence of net charge is referred to as neutral. An object is charged if it has an excess of electrons. The SI derived unit of charge is the coulomb. In electrical engineering, it is common to use the ampere-hour. The symbol Q often denotes charge, early knowledge of how charged substances interact is now called classical electrodynamics, and is still accurate for problems that dont require consideration of quantum effects. The electric charge is a conserved property of some subatomic particles. Electrically charged matter is influenced by, and produces, electromagnetic fields, the interaction between a moving charge and an electromagnetic field is the source of the electromagnetic force, which is one of the four fundamental forces. 602×10−19 coulombs. The proton has a charge of +e, and the electron has a charge of −e, the study of charged particles, and how their interactions are mediated by photons, is called quantum electrodynamics. Charge is the property of forms of matter that exhibit electrostatic attraction or repulsion in the presence of other matter. Electric charge is a property of many subatomic particles. The charges of free-standing particles are integer multiples of the charge e. Michael Faraday, in his electrolysis experiments, was the first to note the discrete nature of electric charge, robert Millikans oil drop experiment demonstrated this fact directly, and measured the elementary charge. By convention, the charge of an electron is −1, while that of a proton is +1, charged particles whose charges have the same sign repel one another, and particles whose charges have different signs attract. The charge of an antiparticle equals that of the corresponding particle, quarks have fractional charges of either −1/3 or +2/3, but free-standing quarks have never been observed. The electric charge of an object is the sum of the electric charges of the particles that make it up. An ion is an atom that has lost one or more electrons, giving it a net charge, or that has gained one or more electrons
27.
Zwitterion
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In chemistry, a zwitterion, formerly called a dipolar ion, is a neutral molecule with both positive and negative electrical charges. Zwitterions are distinct from molecules that have dipoles at different locations within the molecule, zwitterions are sometimes called inner salts. Unlike simple amphoteric compounds that may form either a cationic or anionic species. Amino acids are the examples of zwitterions. These compounds contain an ammonium and a group, and can be viewed as arising via a kind of intramolecular acid–base reaction. NH 2RCHCO 2H ⇌ NH+ 3RCHCO−2 The zwitterionic structure of glycine in the state has been confirmed by neutron diffraction measurements. At least in cases, the zwitterionic form of amino acids also persists in the gas phase. In addition to the acids, many other compounds that contain both acidic and basic centres tautomerize to the zwitterionic form. Examples, such as bicine and tricine, contain a secondary or tertiary amine fragment together with a carboxylic acid fragment. Neutron diffraction measurements show that solid sulfamic acid exists as a zwitterion, many alkaloids, such as LSD and psilocybin, exist as zwitterions because they contain carboxylates and ammonium centres. Many zwitterions contain quaternary ammonium cations, since it lacks N–H bonds, the ammonium center cannot participate in tautomerization. Zwitterions containing quaternary-ammonium centers are common in biology, an example are the betaines. The membrane-forming phospholipids are also commonly zwitterions, the polar head groups in these compounds are zwitterions, resulting from the presence of the anionic phosphate and cationic quaternary ammonium centres. Dipolar compounds and amine oxides are not classified as zwitterions, zwitterionic compounds are neutral compounds having unit electrical charges on atoms
28.
Genetic code
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The genetic code is the set of rules by which information encoded within genetic material is translated into proteins by living cells. Translation is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA molecules to carry amino acids, the genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, with some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme and that scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes exist. While the genetic code determines a proteins amino acid sequence, other genomic regions determine when, efforts to understand how proteins are encoded began after DNAs structure was discovered in 1953. George Gamow postulated that sets of three bases must be employed to encode the 20 standard amino acids used by living cells to build proteins, the Crick, Brenner et al. experiment first demonstrated that codons consist of three DNA bases. Marshall Nirenberg and Heinrich J. Matthaei were the first to reveal the nature of a codon in 1961 and they used a cell-free system to translate a poly-uracil RNA sequence and discovered that the polypeptide that they had synthesized consisted of only the amino acid phenylalanine. They thereby deduced that the codon UUU specified the amino acid phenylalanine, therefore, the codon AAA specified the amino acid lysine, and the codon CCC specified the amino acid proline. Using various copolymers most of the remaining codons were then determined, subsequent work by Har Gobind Khorana identified the rest of the genetic code. Shortly thereafter, Robert W. Holley determined the structure of transfer RNA and this work was based upon Ochoas earlier studies, yielding the latter the Nobel Prize in Physiology or Medicine in 1959 for work on the enzymology of RNA synthesis. Extending this work, Nirenberg and Philip Leder revealed the triplet nature. In these experiments, various combinations of mRNA were passed through a filter that contained ribosomes, unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments, Khorana, Holley and Nirenberg received the 1968 Nobel for their work. The three stop codons were named by discoverers Richard Epstein and Charles Steinberg, amber was named after their friend Harris Bernstein, whose last name means amber in German. The other two stop codons were named ochre and opal in order to keep the color names theme, H. Murakami and M. Sisido extended some codons to have four and five bases. Steven A. Benner constructed a functional 65th codon, in 2016 the first stable semisynthetic organism was created. It was a bacterium with two synthetic bases, in 2017 a mouse engineered with an extended genetic code that can produce proteins with unnatural amino acids was reported. A codon is defined by the initial nucleotide from which starts and sets the frame for a run of successive triplets
29.
Proton
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A proton is a subatomic particle, symbol p or p+, with a positive electric charge of +1e elementary charge and mass slightly less than that of a neutron. Protons and neutrons, each with masses of one atomic mass unit, are collectively referred to as nucleons. One or more protons are present in the nucleus of every atom, the number of protons in the nucleus is the defining property of an element, and is referred to as the atomic number. Since each element has a number of protons, each element has its own unique atomic number. The word proton is Greek for first, and this name was given to the nucleus by Ernest Rutherford in 1920. In previous years, Rutherford had discovered that the nucleus could be extracted from the nuclei of nitrogen by atomic collisions. Protons were therefore a candidate to be a particle, and hence a building block of nitrogen. In the modern Standard Model of particle physics, protons are hadrons, and like neutrons, although protons were originally considered fundamental or elementary particles, they are now known to be composed of three valence quarks, two up quarks and one down quark. The rest masses of quarks contribute only about 1% of a protons mass, the remainder of a protons mass is due to quantum chromodynamics binding energy, which includes the kinetic energy of the quarks and the energy of the gluon fields that bind the quarks together. At sufficiently low temperatures, free protons will bind to electrons, however, the character of such bound protons does not change, and they remain protons. A fast proton moving through matter will slow by interactions with electrons and nuclei, the result is a protonated atom, which is a chemical compound of hydrogen. In vacuum, when electrons are present, a sufficiently slow proton may pick up a single free electron, becoming a neutral hydrogen atom. Such free hydrogen atoms tend to react chemically with other types of atoms at sufficiently low energies. When free hydrogen atoms react with other, they form neutral hydrogen molecules. Protons are spin-½ fermions and are composed of three quarks, making them baryons. Protons have an exponentially decaying positive charge distribution with a mean square radius of about 0.8 fm. Protons and neutrons are both nucleons, which may be together by the nuclear force to form atomic nuclei. The nucleus of the most common isotope of the atom is a lone proton
30.
Conjugate acid
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A conjugate acid, within the Brønsted–Lowry acid–base theory, is a species formed by the reception of a proton by a base—in other words, it is a base with a hydrogen ion added to it. On the other hand, a base is merely what is left after an acid has donated a proton in a chemical reaction. Hence, a base is a species formed by the removal of a proton from an acid. A proton is a particle with a unit positive electrical charge, it is represented by the symbol H+ because it constitutes the nucleus of a hydrogen atom, that is. A cation can be an acid, and an anion can be a conjugate base, depending on which substance is involved. In an acid-base reaction, an acid plus a base reacts to form a conjugate base plus a conjugate acid, refer to the following figure, We say that the water molecule is the conjugate acid of the hydroxide ion after the latter received the hydrogen proton donated by ammonium. On the other hand, ammonia is the base for the acid ammonium after ammonium has donated a hydrogen ion towards the production of the water molecule. The strength of an acid is directly proportional to its dissociation constant. If a conjugate acid is strong, its dissociation will have an equilibrium constant. The strength of a base can be seen as the tendency of the species to pull hydrogen protons towards itself. If a conjugate base is classified as strong, it will hold on to the hydrogen proton when in solution, if a chemical species is classified as a weak acid, its conjugate base will be strong in nature. This can be observed in ammonias reaction with water, the reaction proceeds until most of the ammonia has been transformed to ammonium. This shift to the right in the equilibrium of the reaction means that ammonium does not dissociate easily in water. On the other hand, if a species is classified as a strong acid, an example of this case would be the dissociation of Hydrochloric acid HCl in water. Since HCl is an acid, its conjugate base will be a weak conjugate base. Therefore, in system, most H+ will be in the form of a Hydronium ion H 3O+ instead of attached to a Cl anion. To summarize, the stronger the acid or base, the weaker the conjugate, the acid and conjugate base as well as the base and conjugate acid are known as conjugate pairs. When finding a conjugate acid or base, it is important to look at the reactants of the chemical equation, to identify the conjugate acid, look for the pair of compounds that are related
31.
Ion
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An ion is an atom or a molecule in which the total number of electrons is not equal to the total number of protons, giving the atom or molecule a net positive or negative electrical charge. Ions can be created, by chemical or physical means. In chemical terms, if an atom loses one or more electrons. If an atom gains electrons, it has a net charge and is known as an anion. Ions consisting of only a single atom are atomic or monatomic ions, because of their electric charges, cations and anions attract each other and readily form ionic compounds, such as salts. In the case of ionization of a medium, such as a gas, which are known as ion pairs are created by ion impact, and each pair consists of a free electron. The word ion comes from the Greek word ἰόν, ion, going and this term was introduced by English physicist and chemist Michael Faraday in 1834 for the then-unknown species that goes from one electrode to the other through an aqueous medium. Faraday also introduced the words anion for a charged ion. In Faradays nomenclature, cations were named because they were attracted to the cathode in a galvanic device, arrhenius explanation was that in forming a solution, the salt dissociates into Faradays ions. Arrhenius proposed that ions formed even in the absence of an electric current, ions in their gas-like state are highly reactive, and do not occur in large amounts on Earth, except in flames, lightning, electrical sparks, and other plasmas. These gas-like ions rapidly interact with ions of charge to give neutral molecules or ionic salts. These stabilized species are commonly found in the environment at low temperatures. A common example is the present in seawater, which are derived from the dissolved salts. Electrons, due to their mass and thus larger space-filling properties as matter waves, determine the size of atoms. Thus, anions are larger than the parent molecule or atom, as the excess electron repel each other, as such, in general, cations are smaller than the corresponding parent atom or molecule due to the smaller size of its electron cloud. One particular cation contains no electrons, and thus consists of a single proton - very much smaller than the parent hydrogen atom. Since the electric charge on a proton is equal in magnitude to the charge on an electron, an anion, from the Greek word ἄνω, meaning up, is an ion with more electrons than protons, giving it a net negative charge. A cation, from the Greek word κατά, meaning down, is an ion with fewer electrons than protons, there are additional names used for ions with multiple charges
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Umami
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Umami, or savory taste, is one of the five basic tastes. It has been described as brothy or meaty, people taste umami through taste receptors specific to glutamate. Glutamate is widely present in foods, such as meat broths and fermented products. Since umami has its own rather than arising out of a combination of the traditionally recognized taste receptors. A loanword from the Japanese, umami can be translated as pleasant savory taste and this neologism was coined in 1908 by Japanese chemist Kikunae Ikeda from a nominalization of umai delicious. The compound 旨味 is used for a general sense of a food as delicious. Scientists have debated whether umami was a basic taste since Kikunae Ikeda first proposed its existence in 1908, in 1985, the term umami was recognized as the scientific term to describe the taste of glutamates and nucleotides at the first Umami International Symposium in Hawaii. Umami represents the taste of the amino acid L-glutamate and 5’-ribonucleotides such as guanosine monophosphate and it can be described as a pleasant brothy or meaty taste with a long lasting, mouthwatering and coating sensation over the tongue. The sensation of umami is due to the detection of the anion of glutamate in specialized receptor cells present on the human. Some 52 peptides may be responsible for detecting umami taste and its effect is to balance taste and round out the overall flavor of a dish. Umami enhances the palatability of a variety of foods. Glutamate in acid form imparts little taste, whereas the salts of glutamic acid, known as glutamates. GMP and IMP amplify the taste intensity of glutamate, adding salt to the free acids also enhances the umami taste. Monosodium L-aspartate has an umami taste about four times less intense than MSG whereas ibotenic acid, glutamate has a long history in cooking. In the late-1800s, chef Auguste Escoffier, who opened restaurants in Paris and London, created meals that combined umami with salty, sour, sweet and he did not know the chemical source of this unique quality, however. Umami was first scientifically identified in 1908 by Kikunae Ikeda, a professor of the Tokyo Imperial University and he found that glutamate was responsible for the palatability of the broth from kombu seaweed. He noticed that the taste of kombu dashi was distinct from sweet, sour, bitter, professor Shintaro Kodama, a disciple of Ikeda, discovered in 1913 that dried bonito flakes contained another umami substance. In 1957, Akira Kuninaka realized that the ribonucleotide GMP present in shiitake mushrooms also conferred the umami taste, one of Kuninakas most important discoveries was the synergistic effect between ribonucleotides and glutamate
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Glutamate flavoring
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Glutamate flavoring is a generic name for flavor-enhancing compounds based on glutamic acid and its salts. These compounds provide a taste to food. The sodium salt of glutamic acid, monosodium glutamate is manufactured in a large scale, when glutamic acid or any of its salts is dissolved in water, it immediately forms a solution of separate negative ions called glutamates, and positive ions like H 3O+ or Na+. There is actually a chemical equilibrium among several ionized forms, including zwitterions, at the pH ranges normally occurring in foods, the prevailing ion can be described as −OOC-C-2-COO−, with a net −1 electric charge. Only the glutamate ion is responsible for the taste, so the effect does not depend significantly on the starting compound. However, some crystalline salts such as monosodium glutamate dissolve much better and faster than crystalline glutamic acid, although they occur naturally in many foods, the flavor contributions made by glutamic acid and other amino acids were only scientifically identified early in the twentieth century. The substance was discovered and identified in the year 1866, by the German chemist Karl Heinrich Ritthausen, in 1907 Japanese researcher Kikunae Ikeda of the Tokyo Imperial University identified brown crystals left behind after the evaporation of a large amount of kombu broth as glutamic acid. These crystals, when tasted, reproduced the ineffable but undeniable flavor he detected in many foods, professor Ikeda termed this flavor umami. He then patented a method of mass-producing a crystalline salt of glutamic acid, only the L-glutamate enantiomer has flavor-enhancing properties. Fermented products such as soy sauce, steak sauce, and Worcestershire sauce have levels of glutamate similar to foods with added monosodium glutamate, however, 5% or more of the glutamate may be the D-enantiomer. Nonfermented naturally-occurring foods have lower levels of D-glutamate than fermented products. Glutamate itself is ubiquitous in biological life and it is found naturally in all living cells, primarily in the bound form as a constituent of proteins. Only a fraction of the glutamate in foods is in its free form, Japanese cuisine originally used broth made from kombu to bring up the umami taste in soups. Manufacturers, such as Ajinomoto, use selected strains of Micrococcus glutamicus bacteria in a nutrient-rich medium, the bacteria are selected for their ability to excrete glutamic acid, which is then separated from the nutrient medium and processed into its sodium salt, monosodium glutamate. In the Roman Empire glutamic acid was found in a sauce called garum, the flavor enhancing properties of glutamic acid allowed Romans to reduce the use of expensive salt. The following table illustrates the glutamate content of some selected common foods, free glutamate is metabolized differently from glutamate bound in protein, so they are listed separately. Hydrolyzed proteins, or protein hydrolysates, are acid- or enzymatically treated proteins from certain foods, hydrolyzed protein contains free amino acids, such as glutamate, at levels of 5% to 20%. Hydrolyzed protein is used in the manner as monosodium glutamate in many foods, such as canned vegetables, soups
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Monosodium glutamate
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Monosodium glutamate is the sodium salt of glutamic acid, one of the most abundant naturally occurring non-essential amino acids. Monosodium glutamate is found naturally in tomatoes, cheese and other foods and it was first prepared in 1908 by Japanese biochemist Kikunae Ikeda, who was trying to isolate and duplicate the savory taste of kombu, an edible seaweed used as a base for many Japanese soups. MSG as a flavor enhancer balances, blends, and rounds the perception of other tastes, the U. S. Food and Drug Administration has given MSG its generally recognized as safe designation. The European Union classifies it as a food additive permitted in certain foods, MSG has the HS code 29224220 and the E number E621. Pure MSG is reported not to have a pleasant taste until it is combined with a savory aroma, the basic sensory function of MSG is attributed to its ability to enhance savory taste-active compounds when added in the proper concentration. The optimum concentration varies by food, in soup, the pleasure score rapidly falls with the addition of more than one gram of MSG per 100 mL. The sodium content of MSG, 12%, is about one-third of that in sodium chloride, although other salts of glutamate have been used in low-salt soups, they are less palatable than MSG. A popular belief is that MSG can cause headaches and other feelings of discomfort, MSG has been used for more than 100 years to season food, with a number of studies conducted on its safety. Consumption and manufacture of high-salt and high-glutamate foods, which contain sodium and glutamate, stretch back far longer, with evidence of cheese manufacture as early as 5,500 BC. International and national bodies governing food additives currently consider MSG safe for consumption as a flavor enhancer. Under normal conditions, humans can metabolize relatively large quantities of glutamate, the median lethal dose is between 15 and 18 g/kg body weight in rats and mice, respectively, five times greater than the LD50 of salt. The use of MSG as an additive and the natural level of glutamic acid in foods are not toxicological concerns in humans. According to the report, no support the role of glutamate in chronic disease. A controlled, double-blind, multiple-location clinical trial failed to demonstrate a relationship between the MSG symptom complex and actual MSG consumption, no statistical association has been demonstrated, and the few responses were inconsistent. No symptoms were observed when MSG was administered with food, adequately controlling for experimental bias includes a double-blind, placebo-controlled experimental design and administration by capsule, because of the unique aftertaste of glutamates. In a study by Tarasoff and Kelly,71 fasting participants were given 5 g of MSG, a study by Geha et al. tested the reaction of 130 subjects with a reported sensitivity to MSG. Multiple DBPC trials were performed, with subjects exhibiting at least two symptoms continuing, two people out of the 130 responded to all four challenges. Because of the low prevalence, the researchers concluded that a response to MSG was not reproducible, studies exploring MSGs role in obesity have yielded mixed results
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Radical (chemistry)
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In chemistry, a radical is an atom, molecule, or ion that has an unpaired valence electron. Most radicals are reasonably stable only at low concentrations in inert media or in a vacuum. A notable example of a radical is the hydroxyl radical. Two other examples are triplet oxygen and triplet carbene which have two unpaired electrons, free radicals may be created in a number of ways, including synthesis with very dilute or rarefied reagents, reactions at very low temperatures, or breakup of larger molecules. The latter can be affected by any process that puts energy into the parent molecule, such as ionizing radiation, heat, electrical discharges, electrolysis. Radicals are intermediate stages in many chemical reactions, free radicals play an important role in combustion, atmospheric chemistry, polymerization, plasma chemistry, biochemistry, and many other chemical processes. In living organisms, the free radicals superoxide and nitric oxide and their reaction products regulate many processes, such as control of vascular tone and they also play a key role in the intermediary metabolism of various biological compounds. Such radicals can even be messengers in a process dubbed redox signaling, a radical may be trapped within a solvent cage or be otherwise bound. The qualifier free was then needed to specify the unbound case, following recent nomenclature revisions, a part of a larger molecule is now called a functional group or substituent, and radical now implies free. However, the old nomenclature may still appear in some books, the term radical was already in use when the now obsolete radical theory was developed. Louis-Bernard Guyton de Morveau introduced the phrase radical in 1785 and the phrase was employed by Antoine Lavoisier in 1789 in his Traité Élémentaire de Chimie, a radical was then identified as the root base of certain acids. Historically, the radical in radical theory was also used for bound parts of the molecule. These are now called functional groups, for example, methyl alcohol was described as consisting of a methyl radical and a hydroxyl radical. In a modern context the first organic free radical identified was triphenylmethyl radical and this species was discovered by Moses Gomberg in 1900 at the University of Michigan USA. In 1933 Morris Kharash and Frank Mayo proposed that free radicals were responsible for anti-Markovnikov addition of hydrogen bromide to allyl bromide. It should be noted that the electron of the breaking bond also moves to pair up with the attacking radical electron. Free radicals also take part in addition and radical substitution as reactive intermediates. Chain reactions involving free radicals can usually be divided into three distinct processes and these are initiation, propagation, and termination
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Biosynthesis
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Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds and this process often consists of metabolic pathways. Some of these pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these pathways include the production of lipid membrane components. The prerequisite elements for biosynthesis include, precursor compounds, chemical energy and these elements create monomers, the building blocks for macromolecules. Biosynthesis occurs due to a series of chemical reactions, for these reactions to take place, the following elements are necessary, Precursor compounds, these compounds are the starting molecules or substrates in a reaction. These may also be viewed as the reactants in a chemical process. Chemical energy, chemical energy can be found in the form of high energy molecules and these molecules are required for energetically unfavorable reactions. Furthermore, the hydrolysis of these compounds drives a reaction forward, high energy molecules, such as ATP, have three phosphates. Often, the phosphate is split off during hydrolysis and transferred to another molecule. Catalytic enzymes, these molecules are special proteins that catalyze a reaction by increasing the rate of the reaction, coenzymes or cofactors, cofactors are molecules that assist in chemical reactions. These may be metal ions, vitamin derivatives such as NADH and acetyl CoA, in the case of NADH, the molecule transfers a hydrogen, whereas acetyl CoA transfers an acetyl group, and ATP transfers a phosphate. Two examples of type of reaction occur during the formation of nucleic acids. For some of these steps, chemical energy is required, Precursor molecule + ATP ↽ − − ⇀ product AMP + PP i Simple compounds that are converted into other compounds with the assistance of cofactors. For example, the synthesis of phospholipids requires acetyl CoA, while the synthesis of another component, shingolipids. The general equation for these examples is, Precursor molecule + Cofactor → e n z y m e macromolecule Simple compounds that join together to create a macromolecule, for example, fatty acids join together to form phopspholipids. In turn, phospholipids and cholesterol interact noncovalently in order to form the lipid bilayer and this reaction may be depicted as follows, Molecule 1 + Molecule 2 ⟶ macromolecule Many intricate macromolecules are synthesized in a pattern of simple, repeated structures. For example, the simplest structures of lipids are fatty acids, fatty acids are hydrocarbon derivatives, they contain a carboxyl group “head” and a hydrocarbon chain “tail. ”These fatty acids create larger components, which in turn incorporate noncovalent interactions to form the lipid bilayer
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